The filmmakers commissioned DNA testing on the residue in the boxes said to have held Jesus and Mary Magdalene. There are no bones left, because the religious custom in Israel is to bury archeological remains in a cemetery.

However, the documentary’s director and its driving force, Simcha Jacobovici, an Israeli-born Canadian, said there was enough mitochondrial DNA for a laboratory in Ontario to conclude that the bodies in the “Jesus” and “Mary Magdalene” ossuaries were not related on their mothers’ side. From this, Mr. Jacobovici deduced that they were a couple, because otherwise they would not have been buried together in a family tomb.

In an interview, Mr. Jacobovici was asked why the filmmakers did not conduct DNA testing on the other ossuaries to determine whether the one inscribed “Judah, son of Jesus” was genetically related to either the Jesus or Mary Magdalene boxes; or whether the Jesus remains were actually the offspring of Mary.

“We’re not scientists. At the end of the day we can’t wait till every ossuary is tested for DNA,” he said. “We took the story that far. At some point you have to say, ‘I’ve done my job as a journalist.’ ” (emphasis mine)

Now it seems to me, as a journalist, that Jacobovici’s job as a journalist would be to report on peer-reviewed research published in a scientific journal by a team of experts who had no financial stake in the success of a show. Once he starts commissioning DNA tests of his own, he’s taking on an entirely different set of responsibilities. For example, it’s up to him to make sure that the DNA has not been contaminated by archaeologists (see my post on the diet of Europeans 8,000 years ago). It’s up to him to pass the judgment of scientific experts in the field. And at the very least, it’s up to him to test all the remains–including the ones that supposedly belonged to the son of Jesus. To step back suddenly and say, “I’ve done my job as a journalist” is utterly absurd.

In recent years, scientists have learned a lot about how milk digestion is encoded in the human genome. The lactase gene, LCT, is controlled by neighboring segments of DNA that act like on-off switches. Certain proteins grab onto certain switches, allowing genes to make proteins only under certain conditions. As people grow older, the signals to LCT’s switches change, shutting it down. But in populations where people can digest lactose as adults, mutations to these switches change LCT’s response to signals. Instead of switching off in adulthood, the gene stays on.

About forty years ago, scientists first began to notice that different ethnic groups had different levels of lactase persistence. As they surveyed more groups, a striking pattern emerged: the groups with the highest levels of lactase persistence had traditionally herded cows or other milk-producing animals, while the groups with low levels did not. Some scientists proposed that lactase persistence was the result of recent natural selection. Shutting down lactase production is common not just in people but in all mammals. Before the rise of livestock, it was an adaptive strategy, since lactase were useless after nursing. Once pastoralists had a steady supply of milk, however, digesting milk could boost a person’s odds of survival. Any mutation that allowed a person to absorb more nutrients from milk might be favored by natural selection. In parts of the world where herding never became a way of life, people with the mutation had no advantage.

Scientists have put this hypothesis to the test in a number of ways. As people passed down lactose-associated DNA to their descendants, they also passed down neighboring regions of their genome. Some of those regions are prone to very high rates of mutation. By comparing the mutations in those regions, one team of scientists estimated that lactase persistence first emerged in Europe some time between 7450 and 12,300 years ago. Other researchers have come up with similar estimates by analyzing other DNA segments. These estimates put the origin of lactase persistence back at a time when archaeologists find some of the earliest clues of herding in Europe.

Still, there are other plausible ways to interpret the evidence. Perhaps, for example, human populations were already split up into lactse persistent and non-persistent before the rise of herding. Their different genetic profiles might have even determined which populations ended up herding animals, and which didn’t.

Scientists now have a new way to test hypotheses like this one. Instead of looking at the DNA of living populations and inferring their history, scientists can look at the DNA of people who’ve been dead for thousands of years. A team of scientists based at Mainz University in Germany recently looked for the lactase persistence mutation in ancient bones. They took samples from eight individuals dating back almost 8,000 years. The bones came from sites in Gemrany, Poland, Hungary, and Lithuania. Looking for such a precise bit of DNA is a tricky undertaking, because scientists may end up looking at genes from the archaeologist who found the bones, or even from themselves. So the scientists took pains to confirm that the DNA they extracted really was ancient, such as sequencing their own genes to know what they would look like.

This week the scientists are publishing their results in the Proceedings of the National Academy of Sciences. They found the segment of DNA where the lactase persistence mutation can be found, but in none of the samples did they find the mutation itself. These ancient Europeans, in other words, were lactose intolerant.

A survey of eight people is hardly enough for the scientists to make categorical statements about the genetic makeup of all of Europe. But statistically speaking, it’s striking that the scientists failed to find what is now a common mutation in Europe in people who were separated by many hundreds of miles. The scientists calculate that no more than a third of Europeans could have had the lactase persistence gene at the time, and the true figure could even be zero.

It will be fascinating to see this research grow. As scientists extract more DNA from this period, will they continue to find no mutation? Perhaps they will only find it in one place in Europe–the birthplace, perhaps, of lactase persistence on the continent. And this case, at least, scientists will come closer to seeing human evolution in real time, rather than in retrospect. And if I ever want to pay homage to the ancestors who let me enjoy a fine slice of Gruyere, I’ll know where to go.

“Absence of the Lactase-Persistence associated allele in early Neolithic Europeans” by J. Burger, M. Kirchner, B. Bramanti, W. Haak, and M. G. Thomas. http://www.pnas.org/cgi/doi/10.1073/pnas.0607187104

Communication may work all very well in these cases, but scientists also want to know how they evolved in the first place. Roughly speaking, their question goes something like this. Say you’re an organism living a solitary life. Sending a signal to another member of your species may cost you more than it might bring back in benefits. If you come across some food and suddenly declare, “My, but those are some tasty grubs,” you may find yourself besieged by other members of your species all coming to have some for themselves. You might even attract the attention of a predator and become a meal yourself. So why not just shut up?

There are many ways to attack this question. You can go out and listen to birds. You can genetically engineer bacteria to tinker with their communication system and see what happens. Or you can build an army of robots.

Laurent Keller, an expert on social evolution at the University of Lausanne in Switzerland, chose the latter. Working with robotics experts at Lausanne, he constructed simple robots like the ones shown above. Each robot had a pair of wheeled tracks, a 360-degree light-sensing camera, and an infrared sensor underneath. The robots were controlled by a program with a neural network architecture. In neural networks, inputs come in through various channels and get combined in various combinations, and the combinations then produce outgoing signals. In the case of the Swiss robots, the inputs were the signals from the camera and the infrared sensor, and the output was the control of the tracks.

The scientists then put the robots in a little arena with two glowing red disks. One disk they called the food source. The other was the poison source. The only difference between them was that food source sat on top of a gray piece of paper, and the poison source sat on top of black paper. A robot could tell the difference between the two only once it was close enough to a source to use its infrared sensor to see the paper color.

Then the scientists allowed the robots to evolve. The robots–a thousand of them in each trial of the experiment–started out with neural networks that were wired at random. They were placed in groups of ten in arenas with poison and food, and they all wandered in a haze. If a robot happened to reach the food and detected the gray paper, the scientists awarded it a point. If it ended up by the poison source, it lost a point. The scientists observed each robot over the course of ten minutes and added up all their points during that time. (This part of the experiment was run on a computer simulation to save time and to be able to evolve lots of robots at once.)

In the simplest version of the experiment, the scientists selected the top 200 feeders. Not surprisingly, they were all pretty awful, since they had randomly wired neural networks. But they had promise. The scientists “bred” the robots by creating 100 pairs and using parts of each one’s program to create a new one. Each new program also had a small chance of spontaneously changing in one part (how strongly it reacted to the red light, for example). After several rounds of this mating, the new programs were plugged back into robots, which then groped around again for food. And once again the scientists selected the fastest ones. They repeated this cycle 500 times in 20 different replicate lines. When they were done, they plugged the program into real robots and let them loose in a real arena with real food and poison (well, as real as food and poison get for experimental robots). The real robots behaved just like the simulated ones, demonstrating that the simulation had gotten the physics of the real robots right.

The results were impressive, although perhaps not surprising to people who are familiar with experimental evolution with bacteria. From their randomly wired networks, the robots evolved within a few dozens generations until they were scoring about 160 points a trial. That held in all twenty lines. Each program consists of 240 bits, which means that it could take any of 2 to the 240th power configurations. Out of that unimaginable range of possibilities, the robots in each line found a fast solution.

Now the scientists made things more interesting. There’s a great deal of evidence to suggest that if individuals are closely related to one another, evolution may lead to less cut-throat competition and more cooperation. (See my post on slime molds for an example of this research.) So the scientists ran the robot evolution over again, but this time the robots got kin. Rather than mixing them indiscriminately, they grouped the robots into colonies. They only bred the best performers with other members of their colonies, and from their offspring they created robot clones for the next round of food and poison.

Kinship had a big effect on the robots. Now they were scoring about 170 points. Part of their success was the result of politeness. The scientists designed the food source so that only eight out of ten robots could fit around it at once. The individualist robots jostled for access and ended up all getting fewer points. The robot families, on the other hand, worked together. There was no code of honor in their silicon heads, of course. It’s just that they shared the same instructions.

The scientists then added another wrinkle: they grouped the robots into colonies. There’s evidence to suggest that in some species natural selection can act not just on the level of individuals, but on the level of colonies as well. So the scientists evolved the robots by selecting the best performing colonies, rather than plucking out individuals. And this colony-level selection boosted the robots’ performance even more, scoring an average of 200 points. (A fine point: the scientists also ran the experiment with colony level selection on unrelated robots. They scored 120 points–good but not as good as the others.)

Here, however, is where the experiment got really intriguing. Each robot wears a kind of belt that can glow, casting a blue light. The scientists now plugged the blue light into the robot circuitry. Its neural network could switch the light on and off, and it could detect blue light from other robots and change course accordingly. The scientists started the experiments all over again, with randomly wired robots that were either related or unrelated, and experienced selection as individuals or as colonies.

At first the robots just flashed their lights at random. But over time things changed. In the trials with relatives undergoing colony selection, twelve out of the twenty lines began to turn on the blue light when they reached the food. The light attracted the other robots, bringing them quickly to the food. The other eight lines evolved the opposite strategy. They turned blue when they hit the poison, and the other robots responded to the light by heading away.

Two separate communication systems had evolved, each benefiting the entire colony. By communicating, the robots also raised their score by 14%. Here’s a movie showing six of these chit-chatting robots finding a meal.

A similar robot language arose in two of the other trials (non-relatives with colony selection and relatives with individual selection), although in their cases it didn’t give them as big a boost. A truly perverse language sprang up in the individually selection non-relatives. In all twenty trials, the robots tended to emit blue light when they were far away from the food. The other robots were attracted to them anyway, even if it meant they had to abandon their food.

The scientists speculate that this deception evolved because the robots initially were turning blue at random. Since the only place where a lot of robots would tend to aggregate would be around the food, a strategy evolved to head for the blue light. But that strategy opened up the opportunity for robots to fool each other. If they switched on their blue light when they were away from the food, they would distract other robots, reducing the competition for access to the food. And without kinship to give them a common genetic destiny, the robots got better at fooling one another. In their individualistic scramble, they ended up performing disastrously. Unlike in the other versions of the experiments, the deceptive robots actually scored worse than they did without the chance to evolve communication.

There are lessons both abstract and practical here. The rules that govern social organisms may apply to man-made machines as well. and if you want to avoid a robot uprising, don’t let robots have kids and don’t let them talk to each other.

(Here’s the abstract in Current Biology, and the pdf from Keller’s web site.)

The story of hunting is a lot more complicated today, thanks to a lot of new evidence and some critical reappraisal of the old evidence. Jane Goodall discovered that male chimpanzees hunt monkeys, and since they’re our closest living relatives it’s possible that our ancestors were hunting millions of years before they could stand upright. And in their book Man the Hunted, anthropologists Donna Hart and Robert Sussman argue that for millions of years our hominid ancestors were more likely prey than predator. The oldest stone tools from hominids, dating back 2.6 million years, were likely stone scrapers and other items that were better for scavenging meat than taking down a wildebeest. By 1.5 million years ago, hominids may have been hunting some of their food while stills scavenging other meals. But hunting tools remained very simple for a long time. The oldest wooden spears are 400,000 years old.

And the evidence keeps coming in. Today the journal Current Biology publishes yet another piece of the puzzle: female chimpanzees hunting with spears. More below…

The sight of chimpanzees using tools is hardly new. They’ve been seen making probing sticks for snaring termites, using rocks to bang nuts, and so on. But it was surprising for a team of primatologists to see chimpanzees in Senegal using tools to hunt. On several occasions the scientists saw chimpanzees fashion sticks into spears, which they then rammed into tree hollows where little bushbabies were hiding. In one case, a chimpanzee successfully pinned down a bushbaby and was able to grab it and have a snack.

The discovery adds more weight to the suspicion of some researchers that stone tools can only offer a limited picture of the history of tool use in our ancestors. Ancient hominids might well have been making simple spears and stabbing small animals for millions of years without leaving behind much evidence of their exploits in the fossil record. Studying chimpanzees may offer some clues to what they were up to–particiularly these chimpanzees in Senegal, which live in a mix of woodlands and grasslands that resembles the East African ecosystems where our own ancestors evolved for millions of years.

And what’s particularly intriguing in the report is the fact that of the 22 observed cases of spear-fashioning, only one involved an adult male. Thirteen were carried out by females. (The other cases involved young males.) The scientists suggest that female apes played an important role not only in the development of tools for crushing nuts and catching insects and other kinds of foraging, but also for hunting. Among our earliest ancestors, females might have spent some of their time spearing prey.

If scientists can observe these Amazonian primates some more, it will be interesting to see how much they share their meat. In the forests of the Ivory Coast, scientists have found that when chimps catch small animals they tend to keep the prey for themselves. If the animals are bigger, they’re more likely to share it–willingly or unwillingly–with other chimps. But big game makes up only a small fraction of their calories. Human hunter-foragers, on the other hand, share much more of their food with other members of their group. They also split the work of getting food much more strictly than chimpanzees, with men mostly providing meat and women getting the roots and fruits. Some anthropologists have argued that this division of labor and broader sharing means that humans can have a more reliable supply of food over their lifetime. However, this is not a hard and fast rule. As Harvard anthropologist Frank Marlowe observes, Austrlain females hunt lots of small animals, while men in many cultures are full-time foragers for honey and fruit. There are even cultures in which the men and women hunt together.(pdf) Man, Woman, Hunter, Hunted, Root-Digger, Fruit-Picker–harder to fit on a book cover, but perhaps closer to our complicated reality.

Current Biology has a couple movies you can watch, although they don’t have close-ups of kills. See also National Geographic for more information.

Geology

The study of the earth’s history as revealed in the rocks that make up the earth.[1]

1. Wile, Dr. Jay L. Exploring Creation With General Science. Anderson: Apologia Educational Ministries, Inc. 2000

Vaccine

A weakened or inactive version of a pathogen that stimulates the body’s production of antibodies which can destroy the pathogen.[1]

References

1. Wile, Dr. Jay L. Exploring Creation With General Science. Anderson: Apologia Educational Ministries, Inc. 2000

Isotopes

Two or more atoms that have the same number of protons but different numbers of neutrons.

1. Wile, Dr. Jay L. Exploring Creation With Physical Science. Apologia Educational Ministries, Inc. 1999, 2000

Virus

A non-cellular infectious agent that has two characteristics: It has genetic material inside a protective protein coat, and it cannot reproduce itself.[1]

References

1. Wile, Dr. Jay L. Exploring Creation With Biology. Apologia Educational Ministries, Inc. 1998

What is Apologia Educational Ministries you ask, the ultimate source of scientific information for conservapedia? Their web site sells lots of books for homeschooling, and also includes hand outs that declare,

The Bible Indicates That Humans and Dinosaurs Lived Together. Is there any evidence for this? YES!

Is this what conservatives consider sound science? Is this…wait…what’s this?

Parasite

Parasitism is a form of symbiosis where the parasite benefits and the host is harmed. While it used to be thought that parasites were very simple creatures generally with little impact on their ecosystems, biologists now understand that parasites can be very sophisticated, precisely evolved to take advantage of their hosts and that parasites can have significant effects on their environment and on their host’s evolution. A common parasite in humans is Toxoplasmosis. [1].

References

1. Carl Zimmer’s Parasite Rex

I guess there’s always hope…

[Amazon link shamelessly mine]

Update, Thursday 2/22 10 am: Below the fold, I trace the struggle for Conservapedia’s soul!

Here’s why I love our open source age. We can watch a struggle for Conservapedia’s soul take place. In the comments, Dave Carlson drew attention to a striking change in the entry for parasites. Like Wikipedia, Conservapedia lets the world peer into the discussion behind the changes. Let’s take a look:

On January 3, “DeborahB” wrote the first parasite entry.

An organism that feeds on a living host.[1]

References

1. Wile, Dr. Jay L. Exploring Creation With Biology. Apologia Educational Ministries, Inc. 1998

Then last week on February 15 “JoshuaZ” broke out of the “exploring creation” mold and changed the entry to the one I quoted above, “expanding, replacing inaccurate definition with accurate one.” For a reference, he included Parasite rex.

That’s the definition I saw yesterday when I blogged on it. Then, hours later, “LOrDsSeRvAnt” changed it to the following:

A parasite is an organism that has become dependent on other life forms as a result of the fall. There were no such thing as parasites before the fall, it was only afterwards that they became numerous and now almost every non-parasitic animal on earth has parasites unique to them.

In the history discussion, LOrDsSeRvAnt wrote:

Zimmer is an evolutionist! you can’t trust that guy.

Half an hour later, JoshuaZ stepped in and changed it back to the previous version, with the note,

revert. claim about “fall” was unsourced, nowhere in conservapedia guidelines does it say one can’t use an “evolutionist” as a source or that they can’t be trusted

For the moment, JoshuaZ is prevailing.

The important issue here is not me (although I don’t mind someone spreading the word on my book) but rather how we judge scientific information. LOrDsSeRvAnt is making a mistake that’s all too common these days. He or she seems to think that all you need to do is put a mark on someone–”evolutionist” in this case–and then everything he or she says must be wrong because he or she says it. And anything that is opposite to the marked person’s claims must be right.

In fact, what LOrDsSeRvAnt really ought to do is test my claims by looking at the scientific literature that I cite, or leading college-level textbook such as Foundations of Parasitology. Of course, LOrDsSeRvAnt may not be very happy to discover no mention of “the fall” there, and lots of information on the evolution of parasites. But I can’t help that.

These flat, ribbon-like creatures live inside the digestive tracts of vertebrates. The tapeworms that live in humans can get up to sixty feet long. They feed on our food, despite the fact that they have neither a mouth nor a digestive tract. Their bodies are like a kind of inside-out intestine, rippling with finger-like projections that absorb nutrients. Once inside us, tapeworms can live for decades, deftly escaping the notice of the immune system despite their being as long as an anaconda. Some tapeworms have hooks or suckers on their front end (“head” is too generous a term), which they use to anchor themselves in place. They can also swim upstream to meet food coming out of the stomach and drift back down the intestines to feed, releasing chemicals to slow down their host’s peristalsis so that they don’t get swept away.

Most of a tapeworm’s body is taken up with the equipment for making more tapeworms. Except for its anchoring front end, it is made up of repeating segments, each loaded with male and female sex organs. While the mating habits of tapeworms are a profound mystery, it’s clear that these segments can each produce millions of fertilized eggs. Those eggs have to leave their host to continue the life cycle of the tapeworm; they do so when the segments at the back end of the tapeworm break off and get passed out of the body. The eggs can then be taken up by pigs or cows, where they develop into cysts in their muscle. Eat cyst-infected meat, and you get a tapeworm in your gut. Despite the legends of tapeworm-induced anorexia, most people have no symptoms if they are host to an adult tapeworm. Get a tapeworm egg in you, and you’re in for a totally different experience. The tapeworm may wander through your body and end up in a strange place like your brain, where it grows like a tumor.

We humans are host to 54 species of tapeworms. That’s actually only a tiny fraction of the full diversity of tapeworms, which now stands at about six thousand species. Some live in mammals, others in birds, reptiles, amphibians, and fish. Most tapeworms have elaborate life cycles that take them through an invertebrate, such as a beetle or a crustacean, before passing into a vertebrate. Some travel through three species or more. And along the way, they can manipulate their hosts to ease their path through life. The rat tapeworm develops first in beetles, which they make easier targets for rats. Infected beetles lose the ability to make the toxic chemicals that keep rats at bay, and the beetles become slow to flee from danger. A tapeworm known as Schistocephalus solidus does much the same thing, but underwater. It first infects invertebrates called copepods, which it causes to swim around more, making them easier prey for stickleback fish. Once in the stickleback fish, the tapeworm develops further, getting so big that the fish’s belly swells. Once the tapeworm is ready to move to host number three, the sticklebacks turn bright white and swim boldly, becoming easier prey for water birds. The birds then become hosts to the tapeworms and shed their eggs with their droppings.

Tapeworms are so unlike other animals, so exquisitely adapted to their own way of life, that it can be hard to imagine how they were anything other than tapeworms. In fact, as I described here, the life cycle of tapeworms was discovered by a particularly devout nineteenth-century parasitologist who wanted to demonstrate that God made nothing in vain. As I write in my book Parasite Rex, the evolution of parasites poses a challenge to scientists because they generally don’t leave behind fossils. But they do carry DNA, which scientists can compare to that of other animals. Scientists have been studying the molecular evidence of tapeworm origins for a little over a decade, and a rough picture is emerging. The work is slow, in part because many species of tapeworms and their relatives have yet to be discovered, and scientists have yet to make a careful study of many of the species they have found.

The newest analysis of tapeworms and their relatives has now been published in the journal BMC Evolutionary Biology. It’s the work of Tim Littlewood of the Natural History Museum in London and colleagues in South Korea. The take-home message of the paper is actually a picture, which I’ve reprinted at the bottom of this post. It’s the evolutionary tree of tapeworms and their relatives that emerges from the DNA of these animals. If you follow the tree from its base to the tapeworm branch at the top (“Cestoda”), you are taking the path the ancestors of tapeworms apparently took from free-living animals to superb parasites.

The ancestors of tapeworms were free-living flatworms (platyhelminths). Many flatworms live in the ocean or in fresh water. The transition to parasitism was, not surprisingly, gradual. A group of flatworms called monogeneans are among the closest relatives of tapeworms, and instead of living inside their hosts, they mostly live on the outside. Monogeneans use suckers and hooks to clamp onto a fish. Some grab the gills, other the eyes, others the scales. They then use their mouths to feed on the mucus or blood of their hosts. It appears the monogeneans move from fish to fish, each species of parasite living on a single species of fish host. (Here’s a digression but a good one: some monogeneans give birth to offspring without releasing them from their bodies. Their offspring mature inside them and give birth as well. Like a hideous Russian doll, a monogenean may contain twenty generations of descendents inside its body! ["Kids, it's time you found a place of your own..."])

While monogeneans are close kin to tapeworms, they are not the closest. That dubious honor goes to another group of parasitic flatworms, known as trematodes. They’re commonly called flukes. Many flukes are shaped like leaves, with flat, oval bodies. Like monogeneans, they have powerful suckers for moving around and grasping their hosts, as well as a muscular mouth and throat for feeding.

But instead of living on their hosts, flukes live in them. Blood flukes (schistosomes) live in the blood vessels behind the intestines or bladder of humans. Other flukes set up house in the liver, brain, and other organs of various animals. Another difference between monogenans and flukes are their hosts. Monogeneans have one; flukes generally have two or more. Blood flukes insert their eggs into the human bladder or intestines. Once they reach the outer world, the eggs can infect snails, where they develop into missile shaped forms that then seek out new human flesh. The magnificently grotesque lancet fluke also lives in snails, only to be coughed up by their hosts and then devoured by ants. The ants later crawl up blades of grass, where they are eaten by grazing mammals.

This tree indicates that flukes and tapeworms descend from a flatworm that moved from the outside of its hosts to their inside. This happened a long time ago, judging from the fact that monogeneans, flukes, and tapeworms are found on all sorts of vertebrates except for the oldest lineages represented today by the jawless lampreys and hagfish. When jawed fish first emerged about 450 million years ago, flatworms began their invasion. This ancestral tapefluke may have only needed one host species to complete its life cycle, but afterwards the tapeworms and flukes began to add other species. The tapeworms added arthropods (such as copepods and insects) while the flukes added mollusks such as snails.

It’s possible that the earliest tapeworms were a lot like flukes. Only after they branched off did they lose the sucker found on flukes and monogeneans, for example. Only then did their skin turn into a way to eat. A few clues to the early stages of tapeworm evolution can be gleaned from the oldest lineages of living tapeworms. These tapeworms don’t have repeating segments with male and female organs. Instead, the tapeworms have a single compartment in their body with the sex organs jumbled up inside it. Only after those tapeworms branched off did the sex organs begin to get organized into groups. And only after they were organized into groups, did they get divided into segments.

These “true tapeworms” (known as eucestodes) are the most successful of the group. They’ve thrived by taking advantage of their evolving hosts. They moved ashore with our relatives and infected many species of land vertebrates. Dinosaurs probably had tapeworms too, and we can only wonder how long they got. When whales and other vertebrates returned to the water, they took tapeworms with them. In the evolutionary trees of tapeworms, scientists can see the collisions of continents, the openings of oceans. Tapeworms shuffled between host species as well. Our own ancestors may have acquired the most common human tapeworm (Taenia solium) from the carcasses that hominids scavenged with stone tools a million years ago.

This tree is different in some important ways from previous versions, which isn’t surprising since it is based on more data. Littlewood and other researchers will be testing it with still more data–other species, other genes. And while this tree offers a series of steps from free-living flatworm to gut-dwelling tapeworm, many steps in between remain to be documented. Of course, that’s the case with any evolutionary transition, whether it’s whales moving to sea or hominids becoming human. In this case, perhaps some of those steps will be filled in with the discovery of new species of tapeworms and their relatives. Perhaps down in some unexplored chasm in the deep sea there’s some fish swimming around with a parasite that’s not quite tapeworm, not quite fluke: a living piece of history.

Top image courtesy of Darlyne Murawski

The discovery of H. pylori’s role in ulcers attracted a huge amount of attention to the bug, and to its effects on different people. In the late 1990s Mark Achtman, a German microbiologist at the Max Planck Institut for Infectious Biology, began to gather strains of H. pylori from around the world. He and his colleagues compared the DNA from the strains to see how they were related to one another. They found something strange. Most of the H. pylori strains they collected in China and Japan appeared to be closely related to one another. Based on the diversity of these Asian germs, Achtman suggested they had arrived in the stomachs of early Homo sapiens that moved into Asia some 40,000 years ago.

Further research by Achtman and others indicated that other ethnic groups also carried their own strains of H. pylori. A debate then emerged about how germ and host got associated in this way. H. pylori is not like the flu, which can move between continents in a matter of days. Scientists don’t know much about how it gets from stomach to stomach, but it seems to move mostly within families. So it would make sense that H. pylori’s genealogy tracked the genealogy of its hosts. On the other hand, some critics have argued, H. pylori might be a recent arrival in our stomachs. If it jumped from animals to humans on several occasions in different parts of the world, it might have produced the same patterns seen by Achtman and others.

In this week’s Nature, Achtman and his colleagues report the latest data on humans and their ulcer bugs. They argue that our histories are even more intimately wrapped together than previously thought…

Achtman now has H. pylori DNA from 769 people from 51 ethnic groups, spanning the world from the Finland to Samoa. He and his colleagues used this information to draw an evolutionary tree of the bacteria. They found that the bacteria fell into five major populations. (See figure b at the bottom of this post, which comes from the paper.) The scientists then made a careful study of where the people who carried strains from those five branches live, and used that information to determine where each branch originated. The deepest branch of the H. pylori tree originated in East Africa (Ancestral Africa 2, fig. g). Two younger branches are closely related to one another–one originating in west Africa (Ancestral Africa1, fig. f) and another in North Africa (AE2, fig. e). Another branch originated in India (AE1, fig. c) and is closely related to a branch found in East Asia and the New World (Ancestral EastAsia, fig. d).

This pattern, Achtman and his colleagues argue, bears a striking resemblance to the expansion of our own species over the past 100,000 years. A number of studies on human DNA (such as this one) indicate that Homo sapiens expanded from a small base in East Africa. At first they moved out through Africa, but then after about 60,000 years ago some populations pushed out into the Near East and then into Europe and Asia, and finally into the New World. The human genetic diversity found in Africa is greater than in the rest of the world, because humans have deeper roots there. Very small populations moved into other continents, and as a result, their genetic diversity is lower. In fact, the further away you go from Africa, the lower the genetic diversity gets. (Some scientists disagree, it should be pointed out.) Like humans, H. pylori has the greatest genetic diversity in Africa, and the further from Africa you go, the less diverse it gets.

Achtman and his colleagues built statistical models to figure out how best to explain the patterns they’ve found in H. pylori DNA. They conclude that early humans already carried H. pylori in their stomachs. (How bad their ulcers were the scientists don’t say.) When people began expanding from East Africa, they took H. pylori with them, and ultimately they carried the bacteria across the world. The major branches of H. pylori that Achtman and his colleagues identified emerged during later population booms. The scientists can even detect the arrival of different strains of H. pylori in Europe as successive waves of human immigrants moved into the continent. Because H. pylori is so unadventurous when it comes to infecting new hosts, it has become a chronicler of our past.

H. pylori even has something to say about the ever-controversial matter of race. When scientists were first gathering up information on H. pylori, the geographical differences seemed stark. The bacteria in Europe were distinct from the ones in Asia or Africa. Scientists studying human DNA had much the same experience. They found that by examining certain genetic markers they could accurately predict which continent a person came from. But other scientists challenged these results. They argued that the data in the early studies were far from a representative sample of the world’s human genetic diversity. These scientists put together their own collection of human DNA and concluded that the clusters blurred smoothly into each other.

H. pylori is now blurring as well. The chart in figure a below shows the different strains of H. pylori found in different human populations (the colors correspond to the branches of the tree in figure b). The people in different parts of the world have their own distinctive blend of bacteria, but for the most part one blend blends into the next, forming a continuum from Africa to the New World. Even in our ulcers, we are not so different after all.

(Paper link to come; doi:10.1038/nature05562)